This is really several questions conflated into one.
1) Why are Portuguese Azores and Madeira coins from 1980 listed under Portugal? Because they're Portuguese coins - they were legal tender in the whole of Portugal, and Azores and Madeira were not sufficiently autonomous
in 1980 to issue their own coinage. Those coins are actually of similar status to the US territory quarters from 2010. Krause made a mistake here.
However, Azores
used to be sufficiently autonomous to issue their own coinage until the early 20th century (and, apparently, for a short period in the mid-19th century, so was Madeira), and such coins are, in fact, listed on Numista under the respective issuers (in turn grouped under Portugal).
2) Why are British Antarctic Territory and British Indian Ocean Territory separate
issuers? Because they are
still (considered) sufficiently autonomous to issue their own coinage, as are Jersey, Isle of Man, Falkland Islands, and a bunch of other British territories not part of mainland UK.
There's a bit of a gray area here involving the likes of Gough Island - there's some debate as to whether the coins naming (mostly unpopulated) islands near Tristan da Cunha, such as
this type, should be counted as separate issuers corresponding to the named islands (their Krause status), as (non-circulating) commemorative coins of Tristan da Cunha itself (their current Numista status), or perhaps even as exonumia (i.e. fantasy issues). BAT and BIOT are pretty clearly of similar status to Falklands, though.
3) Why are British Antarctic Territory and British Indian Ocean Territory (and Falkland Islands, for that matter) separate
countries? I have no good answer to this; Hong Kong is listed under China (where it admittedly probably
should be listed - for now, at least) despite being clearly separate in terms of coinage, but French Polynesia is listed as its own country even though it is certainly French territory. (And what's up with American Samoa?)
If we were 100% consistent, BAT, BIOT, and Falklands (and probably even Jersey) would almost certainly have been listed under the UK, while French Polynesia and New Caledonia would probably have been listed under France. Not sure if that's the correct way to go about it, though.
The
really weird placement is probably the British West Indies; by all rights they should probably count as their own first-level country, especially since much of them isn't even British territory now. I dunno who decided to count them (and
only them, aside from the obvious England and Scotland) under the UK.
(Wales would probably have been grouped under the UK if it was listed as a Numista issuer, but it is not currently listed; they seem to have only ever made
one known type, which might not even actually be Welsh, so perhaps their current absence is correct. Northern Ireland was never sufficiently autonomous for its own coinage, though it does issue its own banknotes.)
And while we're at that, I'll continue to mention my own bugbear - Isles de France and Bonaparte [sic]. A one-coin issuer with one really rare type, it had counted as its own country
since at least June 2011, and somehow still does to this day; yet there's quite a bit of evidence that it should not even technically be its own
issuer, much less its own country.
In particular, coins from the coterminous Isles de France et de Bourbon (such as
this type) are listed under Reunion today.
